Genome-data-of-Hanfu-apple

FASTA files of chromosomes and genes, gff files for gene models, scripts.

Genome data

1. HFTH1.genome.fa The assembled genome sequences (Pseudo-chromosomes) with fasta format of 'Hanfu' apple.

2. HFTH1.gene.gff3.gz Gff files for gene models

3. HFTH1.gene.cds.fa.gz Coding sequences for gene models

4. HFTH1.gene.pep.fa.gz Protein sequences for gene models.

Script:

1. stat N50-N90 value of contigs and scaffolds: genomeN50.py

2. repeat annotation with Repeatmodeler: Run_DenovoRepeatFinder.pl

3. repeat annotation with RepeatMasker, RepeatProteinMask, Trf: Run_Repeat_Protein_Mask_Trf.pl

4. mask repeat region with N: Run_remask.pl

5. stat Repeat results: Run_RepeatStatistic.py

6. gap filling: gap.fill.sh gap.fill.step1.py gap.fill.step2.py